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- PDB-8y2y: MPXV mRNA capping enzyme small subunit -

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Basic information

Entry
Database: PDB / ID: 8y2y
TitleMPXV mRNA capping enzyme small subunit
ComponentsmRNA-capping enzyme regulatory subunit OPG124
KeywordsTRANSFERASE / small subunit
Function / homologyPoxvirus mRNA capping enzyme, small subunit / Poxvirus mRNA capping enzyme, small subunit superfamily / Poxvirus mRNA capping enzyme, small subunit / DNA-templated transcription termination / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / mRNA-capping enzyme regulatory subunit OPG124
Function and homology information
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, A.K. / Li, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Emerg Microbes Infect / Year: 2024
Title: Structural basis of the monkeypox virus mRNA cap N7 methyltransferase complex.
Authors: Chen, A. / Fang, N. / Zhang, Z. / Wen, Y. / Shen, Y. / Zhang, Y. / Zhang, L. / Zhao, G. / Ding, J. / Li, J.
History
DepositionJan 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA-capping enzyme regulatory subunit OPG124


Theoretical massNumber of molelcules
Total (without water)33,5001
Polymers33,5001
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.242, 77.242, 96.944
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

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Components

#1: Protein mRNA-capping enzyme regulatory subunit OPG124 / Virus termination factor small subunit / mRNA-capping enzyme 33 kDa subunit / mRNA-capping enzyme ...Virus termination factor small subunit / mRNA-capping enzyme 33 kDa subunit / mRNA-capping enzyme D12 subunit / mRNA-capping enzyme small subunit


Mass: 33499.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG124, MPXVgp109 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H0DN96
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.0M Ammonium sulfate, 0.1M CAPS/Sodium hydroxide pH 10.5, 0.2M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.14→66.89 Å / Num. obs: 18965 / % possible obs: 100 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 2.217
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 18965 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→66.89 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 32.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2715 871 4.99 %
Rwork0.2024 --
obs0.2059 17447 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→66.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 0 72 2327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152298
X-RAY DIFFRACTIONf_angle_d1.5843108
X-RAY DIFFRACTIONf_dihedral_angle_d12.496302
X-RAY DIFFRACTIONf_chiral_restr0.062358
X-RAY DIFFRACTIONf_plane_restr0.012390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.3121460.25382707X-RAY DIFFRACTION100
2.34-2.520.30651210.20622730X-RAY DIFFRACTION100
2.52-2.770.28591470.26142722X-RAY DIFFRACTION100
2.77-3.170.31461460.22542757X-RAY DIFFRACTION100
3.17-3.990.2861540.20122762X-RAY DIFFRACTION100
4-66.890.23341570.17452898X-RAY DIFFRACTION100

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